The tenses in 1 and 3 are right.
In 2, the tenses are correct if you mean (in both sentences) that she is not happy anymore.
1. He tells me that she is happy.
=> He told me that she was happy.
2. He has told me that she was happy.
=> He told me that she had been happy.
3. He will tell me that she will be happy.
=> He told me that she would be happy.
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Q1: According to the change of the tense in the main clause, the tense in the subordinate clause changes as above? Is that right?
Q2: In #2, in the first sentence, is there no problem in using the verbs?
Q2:
2 answers
http://grammar.ccc.commnet.edu/grammar/verbs.htm#sequence
http://www.englishgrammar.org/sequence-tenses/
http://www.englishgrammar.org/sequence-tenses/